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HakaiInstitute / jsp-time-series-report

Juvenile salmon program annual time series
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Updated data wrangle & sea lice to refer to data package files #19

Closed jclgan closed 5 years ago

jclgan commented 5 years ago

Edits to data_wrangle.rmd: Instead of {r setup} and {r sealice} referring to the hakaisalmon R package, they now refer to the .csv files in https://github.com/HakaiInstitute/jsp-data-packages.

Applied filter(yday < 190) to 2019 field data so it is restricted to the same sampling date range as 2015-2018 data.

Due to sea louse data in the data package having different table structure than in hakaisalmon, script has been updated to produce the same output format.

No changes have been made to {r sealice bootstrapping} as Brett should review the code.

jclgan commented 5 years ago

Note that since the data package files are stored in another repository/R project, I had to use absolute filepaths instead of here::here(). Is there a way to call on the files in the data package, or would we need to version the package and read in the .csvs to store in this project repo?

jclgan commented 5 years ago

It looks like most of the sample sizes in sealice_summary_table increased. How did that happen?

With the exception of 36 fish, it looks like none of the fish that were field loused only were included in the original time series summary.

The 36 other fish belong to three packages, which don't seem out of the ordinary upon inspection (within the date range, approved sites, received lab and/or field louse ID, and have corresponding records)